Difference between revisions of "Team:Peking/test"

 
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                            <img src="https://static.igem.org/mediawiki/2017/f/f5/Wojiushishishi.png" alt="INTELLIGENE" style="max-width: 800px;" />
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                                 What will you do if you could <b>reprogram</b>cells and design there <b>life processes</b>?
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                                 What will you do if you could <b>reprogram</b> cells and design there <b>life processes</b>?
 
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                                 A medical patch that can <b>heal</b> patients with faulty methabolic pathways?
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                                 Cells that can <b>survive</b> in harsh environements by doing a series of functions their surroundings going where <b>no cells have gone before</b>?
 
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                                Cells that can <b>survive</b> in harsh environements by making complex calculations about their surroundings going where <b>no cells have gone before</b>?
 
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                 <h2><span>Why </span>genetic circuits ?</h2>
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                 <h2><span>Why </span>sequential logic?</h2>
 
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                     <p class="sub-lead">As synthetic biologists, we are constantly striving to change and understand the world around us. Whether it be the creation of biosensors for drugs or cellular environments, or the creation of new, highly specialized cells, many of the problems facing synthetic biologists today can be solved through the creation of cells with synthetic or partly-synthetic genetic networks. These cells can be taught to make calculations that they have never done before. They can produce new proteins, but also take combinations of inputs and have a predictable output, essentially “making decisions” based on cellular information. The applications are boundless, but this technology is not ready yet. Intelligene represents a concerted effort by a group of students to create new tools - and refine old ones – geared towards the creation of synthetic genetic networks. Follow our journey through a spectacular summer below.
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                     <p class="sub-lead">Cells are responsive to a myriad signals under most conditions and adjust their own internal mechanisms order to survive. This adjustment depends not only on processing a combination of current environmental signal inputs , but also on determining the cell’s current state, which is a result of a series of past inputs.  In digital circuit theory, this operating mode is known as <b>sequential logic</b>. Nowadays, a wide variety of tasks can be performed by synthetically engineered genetic circuits, mostly constructed using combinational logic. Contrast to sequential logic, it's output is a function of the present input only. It is difficult to perform functions in a specific order, which has limited the widespread implementation of such systems. The ability of sequential logic circuits to store modest amounts of information within living systems and to act upon them would enable new approaches to the study and control of biological processes . A cell can be designed to do work that is more complex if it has more states. In other words, we can reach a new dimensionality in designing synthetic life – <b>time</b>.
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                     <p class="sub-lead">Intelligene is best thought of as a suite of tools, combining aspects of computational biology and synthetic biology to help scientists with new dCas9-based genetic circuits, from their design all the way through to their implementation.
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                     <p class="sub-lead">This year, the Peking iGEM team is attempting to develop a frame of biological sequential circuits that are programmable. The envisioned circuit is capable of both storing states in DNA and automatically running a series of instructions in a specific order. More specifically, the sequential logic that consists of a <b>clock</b> , <b>flip flop</b>  and <b>control unit</b> in bacteria. The clock is an oscillator with a repeated signal cycle that is utilized like a metronome to trigger actions of sequential logic circuits. <b>Flip-flop</b> is a memory device that can remember a state. Paired with a clock signal, it can realize state transition. The <b>control unit</b> is a functional part which can convert a signal from flip-flop into complex functions. With such a design, historical events are recorded and influence current cell behavior.</p>
                    </p>
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<p class="sub-lead">This work tries to point the way toward building large computational sys-tems from modular biological parts—basic sequential computing devices in living cells—and ultimately, programming complex biological functions. Computers have thus become "alive". A unicellular organism itself cannot pack much computational power, but considered as a modular building block, its potential is impressive.
                    <p class="sub-lead">In order to help with the intelligent and intuitive design of these circuits, we decided to modify a recently-published program called Cello. Cello works by combining information about the circuit the user wants to create, and biological information about the system the user is building the circuit for, with a series of algorithms which produce a plasmid which contains an optimized biological form of that circuit. While we loved the concept and its powerful design, we thought that certain aspects could be built upon to increase user-friendliness and embellish its open-source nature. To this end, we created a new, simple, graphical user interface, and connected Cello with databases we created, which make the information it uses public and easily transferrable between users.
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                    <p class="sub-lead ">Once a circuit is designed, biological gates are needed to make that circuit. These gates essentially take a simple combination of inputs and produce a given output, according to some rule. Many currently used gates are based on transcription factors, but the use of artificial transcription factors, built using dCas9, is becoming more commonplace as these transcription factors can be reprogrammed to be specific to a certain target and their effect can be fine-tuned by selecting appropriate transcriptional effectors to use within them. During our project we successfully used an architecture first described by Zalatan et al. (2015) to reproduce a previously described activating artificial transcription factor. We also produced two novel repressing artificial transcription factors. Using these parts, we developed two novel NOT gates, each with differing designs.
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Latest revision as of 01:13, 17 November 2017

iGEM EPFL 2016

INTELLIGENE

What will you do if you could reprogram cells and design there life processes?

A periodic drug delivery to precise drug release in sequential order, appropriate time?

An automatic cell factory where all biosynthetic procedures in one fermentation tank?

Cells that can survive in harsh environements by doing a series of functions their surroundings going where no cells have gone before?

Why sequential logic?


Cells are responsive to a myriad signals under most conditions and adjust their own internal mechanisms order to survive. This adjustment depends not only on processing a combination of current environmental signal inputs , but also on determining the cell’s current state, which is a result of a series of past inputs. In digital circuit theory, this operating mode is known as sequential logic. Nowadays, a wide variety of tasks can be performed by synthetically engineered genetic circuits, mostly constructed using combinational logic. Contrast to sequential logic, it's output is a function of the present input only. It is difficult to perform functions in a specific order, which has limited the widespread implementation of such systems. The ability of sequential logic circuits to store modest amounts of information within living systems and to act upon them would enable new approaches to the study and control of biological processes . A cell can be designed to do work that is more complex if it has more states. In other words, we can reach a new dimensionality in designing synthetic life – time.

What we did


This year, the Peking iGEM team is attempting to develop a frame of biological sequential circuits that are programmable. The envisioned circuit is capable of both storing states in DNA and automatically running a series of instructions in a specific order. More specifically, the sequential logic that consists of a clock , flip flop and control unit in bacteria. The clock is an oscillator with a repeated signal cycle that is utilized like a metronome to trigger actions of sequential logic circuits. Flip-flop is a memory device that can remember a state. Paired with a clock signal, it can realize state transition. The control unit is a functional part which can convert a signal from flip-flop into complex functions. With such a design, historical events are recorded and influence current cell behavior.

This work tries to point the way toward building large computational sys-tems from modular biological parts—basic sequential computing devices in living cells—and ultimately, programming complex biological functions. Computers have thus become "alive". A unicellular organism itself cannot pack much computational power, but considered as a modular building block, its potential is impressive.